I hit a dear today and I had to take my wheel well out on the passenger side and was noticing that the my k&N is right there and was seeing if any one has made some kind of patch the 2 wholes that are important?

I have been running without the inners for a few months now. The engine bay get dirtier and you can hear the engine a little more. I am planning on making some kind of filler for the two spaces leading into the engine bay. I have the Volant intake so my filter isn't exposed like yours. If you get yourself a DryCharger then it wouldn't be so bad.